A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2023-12-14, 17:16 PST based on data in:
/home/cmacdonald/NGS/gpr68_dec2022/results/gpr68_dec2022/gatk/home/cmacdonald/NGS/gpr68_dec2022/stats/gpr68_dec2022/processing/home/cmacdonald/NGS/gpr68_dec2022/stats/gpr68_dec2022/fastqc/home/cmacdonald/NGS/gpr68_dec2022/stats/gpr68_dec2022
General Statistics
Showing 166/166 rows and 3/6 columns.| Sample Name | % Dups | % GC | M Seqs |
|---|---|---|---|
| Surface_26_S26_R1_001 | 95.3% | 55% | 10.6 |
| Surface_26_S26_R2_001 | 93.5% | 55% | 10.6 |
| Surface_27_S27_R1_001 | 96.2% | 55% | 13.1 |
| Surface_27_S27_R2_001 | 92.5% | 55% | 13.1 |
| Surface_28_S28_R1_001 | 96.7% | 56% | 13.9 |
| Surface_28_S28_R2_001 | 94.6% | 55% | 13.9 |
| Surface_29_S29_R1_001 | 95.6% | 55% | 9.3 |
| Surface_29_S29_R2_001 | 93.7% | 55% | 9.3 |
| Surface_55_S55_R1_001 | 96.0% | 57% | 14.7 |
| Surface_55_S55_R2_001 | 93.9% | 56% | 14.7 |
| Surface_56_S56_R1_001 | 95.8% | 57% | 12.0 |
| Surface_56_S56_R2_001 | 93.5% | 58% | 12.0 |
| Surface_57_S57_R1_001 | 95.9% | 55% | 9.3 |
| Surface_57_S57_R2_001 | 92.3% | 56% | 9.3 |
| Surface_58_S58_R1_001 | 96.3% | 55% | 11.9 |
| Surface_58_S58_R2_001 | 93.2% | 55% | 11.9 |
| Surface_81_S81_R1_001 | 94.5% | 55% | 7.4 |
| Surface_81_S81_R2_001 | 93.5% | 55% | 7.4 |
| Surface_82_S82_R1_001 | 95.7% | 58% | 8.8 |
| Surface_82_S82_R2_001 | 94.3% | 58% | 8.8 |
| Surface_83_S83_R1_001 | 95.7% | 59% | 9.0 |
| Surface_83_S83_R2_001 | 94.3% | 60% | 9.0 |
| nontreated_1_S1_R1_001 | 96.5% | 56% | 19.6 |
| nontreated_1_S1_R2_001 | 93.2% | 56% | 19.6 |
| nontreated_30_S30_R1_001 | 96.1% | 56% | 13.8 |
| nontreated_30_S30_R2_001 | 92.7% | 56% | 13.8 |
| pH55_2_S2_R1_001 | 95.4% | 57% | 13.6 |
| pH55_2_S2_R2_001 | 92.4% | 56% | 13.6 |
| pH55_31_S31_R1_001 | 95.9% | 56% | 14.5 |
| pH55_31_S31_R2_001 | 94.8% | 57% | 14.5 |
| pH55_32_S32_R1_001 | 96.1% | 56% | 13.6 |
| pH55_32_S32_R2_001 | 93.4% | 57% | 13.6 |
| pH55_33_S33_R1_001 | 95.8% | 59% | 13.5 |
| pH55_33_S33_R2_001 | 95.4% | 58% | 13.5 |
| pH55_34_S34_R1_001 | 96.6% | 59% | 13.5 |
| pH55_34_S34_R2_001 | 94.9% | 57% | 13.5 |
| pH55_3_S3_R1_001 | 96.2% | 58% | 15.9 |
| pH55_3_S3_R2_001 | 94.4% | 57% | 15.9 |
| pH55_4_S4_R1_001 | 96.0% | 56% | 13.3 |
| pH55_4_S4_R2_001 | 93.1% | 55% | 13.3 |
| pH55_59_S59_R1_001 | 96.4% | 57% | 13.9 |
| pH55_59_S59_R2_001 | 93.9% | 56% | 13.9 |
| pH55_5_S5_R1_001 | 96.1% | 55% | 11.1 |
| pH55_5_S5_R2_001 | 92.8% | 55% | 11.1 |
| pH55_60_S60_R1_001 | 96.2% | 57% | 12.8 |
| pH55_60_S60_R2_001 | 94.2% | 57% | 12.8 |
| pH55_61_S61_R1_001 | 96.4% | 57% | 14.6 |
| pH55_61_S61_R2_001 | 94.8% | 57% | 14.6 |
| pH55_62_S62_R1_001 | 93.2% | 57% | 11.8 |
| pH55_62_S62_R2_001 | 92.9% | 56% | 11.8 |
| pH55ogr_35_S35_R1_001 | 94.9% | 56% | 10.4 |
| pH55ogr_35_S35_R2_001 | 93.8% | 55% | 10.4 |
| pH55ogr_36_S36_R1_001 | 96.2% | 57% | 14.2 |
| pH55ogr_36_S36_R2_001 | 94.2% | 56% | 14.2 |
| pH55ogr_37_S37_R1_001 | 96.7% | 58% | 15.5 |
| pH55ogr_37_S37_R2_001 | 94.4% | 57% | 15.5 |
| pH55ogr_38_S38_R1_001 | 96.3% | 56% | 12.0 |
| pH55ogr_38_S38_R2_001 | 93.2% | 56% | 12.0 |
| pH55ogr_63_S63_R1_001 | 96.2% | 58% | 14.3 |
| pH55ogr_63_S63_R2_001 | 94.7% | 58% | 14.3 |
| pH55ogr_64_S64_R1_001 | 95.8% | 56% | 16.9 |
| pH55ogr_64_S64_R2_001 | 95.2% | 57% | 16.9 |
| pH55ogr_65_S65_R1_001 | 94.8% | 56% | 7.2 |
| pH55ogr_65_S65_R2_001 | 95.2% | 56% | 7.2 |
| pH55ogr_6_S6_R1_001 | 96.4% | 56% | 19.6 |
| pH55ogr_6_S6_R2_001 | 93.7% | 56% | 19.6 |
| pH55ogr_7_S7_R1_001 | 96.2% | 56% | 12.9 |
| pH55ogr_7_S7_R2_001 | 92.3% | 56% | 12.9 |
| pH55ogr_8_S8_R1_001 | 95.4% | 55% | 11.5 |
| pH55ogr_8_S8_R2_001 | 92.4% | 55% | 11.5 |
| pH55ogr_9_S9_R1_001 | 95.0% | 57% | 8.8 |
| pH55ogr_9_S9_R2_001 | 95.4% | 57% | 8.8 |
| pH65_18_S18_R1_001 | 94.4% | 55% | 10.1 |
| pH65_18_S18_R2_001 | 90.6% | 55% | 10.1 |
| pH65_19_S19_R1_001 | 96.2% | 56% | 13.9 |
| pH65_19_S19_R2_001 | 92.8% | 55% | 13.9 |
| pH65_20_S20_R1_001 | 95.7% | 56% | 12.8 |
| pH65_20_S20_R2_001 | 94.0% | 56% | 12.8 |
| pH65_21_S21_R1_001 | 89.2% | 64% | 13.7 |
| pH65_21_S21_R2_001 | 88.0% | 64% | 13.7 |
| pH65_47_S47_R1_001 | 96.1% | 57% | 13.3 |
| pH65_47_S47_R2_001 | 93.3% | 56% | 13.3 |
| pH65_48_S48_R1_001 | 96.5% | 57% | 15.9 |
| pH65_48_S48_R2_001 | 93.7% | 57% | 15.9 |
| pH65_49_S49_R1_001 | 96.5% | 56% | 16.7 |
| pH65_49_S49_R2_001 | 93.9% | 56% | 16.7 |
| pH65_50_S50_R1_001 | 90.9% | 61% | 15.0 |
| pH65_50_S50_R2_001 | 89.7% | 60% | 15.0 |
| pH65_73_S73_R1_001 | 94.3% | 59% | 8.7 |
| pH65_73_S73_R2_001 | 92.6% | 58% | 8.7 |
| pH65_74_S74_R1_001 | 94.4% | 56% | 6.9 |
| pH65_74_S74_R2_001 | 91.9% | 56% | 6.9 |
| pH65_75_S75_R1_001 | 95.1% | 60% | 7.1 |
| pH65_75_S75_R2_001 | 93.7% | 59% | 7.1 |
| pH65_76_S76_R1_001 | 88.7% | 59% | 7.7 |
| pH65_76_S76_R2_001 | 89.3% | 59% | 7.7 |
| pH65ogr_22_S22_R1_001 | 95.5% | 55% | 9.8 |
| pH65ogr_22_S22_R2_001 | 92.4% | 55% | 9.8 |
| pH65ogr_23_S23_R1_001 | 96.3% | 57% | 12.9 |
| pH65ogr_23_S23_R2_001 | 92.6% | 57% | 12.9 |
| pH65ogr_24_S24_R1_001 | 95.2% | 57% | 10.9 |
| pH65ogr_24_S24_R2_001 | 94.4% | 57% | 10.9 |
| pH65ogr_25_S25_R1_001 | 91.9% | 60% | 13.1 |
| pH65ogr_25_S25_R2_001 | 92.2% | 59% | 13.1 |
| pH65ogr_51_S51_R1_001 | 96.5% | 57% | 15.2 |
| pH65ogr_51_S51_R2_001 | 94.3% | 56% | 15.2 |
| pH65ogr_52_S52_R1_001 | 96.4% | 56% | 12.6 |
| pH65ogr_52_S52_R2_001 | 93.6% | 56% | 12.6 |
| pH65ogr_53_S53_R1_001 | 95.4% | 56% | 11.1 |
| pH65ogr_53_S53_R2_001 | 95.0% | 57% | 11.1 |
| pH65ogr_54_S54_R1_001 | 95.2% | 56% | 15.3 |
| pH65ogr_54_S54_R2_001 | 92.2% | 57% | 15.3 |
| pH65ogr_77_S77_R1_001 | 95.4% | 55% | 6.7 |
| pH65ogr_77_S77_R2_001 | 92.2% | 55% | 6.7 |
| pH65ogr_78_S78_R1_001 | 95.2% | 56% | 7.3 |
| pH65ogr_78_S78_R2_001 | 90.3% | 56% | 7.3 |
| pH65ogr_79_S79_R1_001 | 95.7% | 56% | 8.5 |
| pH65ogr_79_S79_R2_001 | 92.4% | 56% | 8.5 |
| pH65ogr_80_S80_R1_001 | 93.1% | 57% | 7.2 |
| pH65ogr_80_S80_R2_001 | 92.6% | 57% | 7.2 |
| pH6_10_S10_R1_001 | 95.3% | 56% | 12.9 |
| pH6_10_S10_R2_001 | 93.0% | 56% | 12.9 |
| pH6_11_S11_R1_001 | 95.2% | 56% | 11.8 |
| pH6_11_S11_R2_001 | 92.9% | 56% | 11.8 |
| pH6_12_S12_R1_001 | 96.1% | 57% | 14.8 |
| pH6_12_S12_R2_001 | 93.5% | 56% | 14.8 |
| pH6_13_S13_R1_001 | 92.3% | 63% | 15.1 |
| pH6_13_S13_R2_001 | 91.5% | 61% | 15.1 |
| pH6_39_S39_R1_001 | 96.4% | 58% | 15.3 |
| pH6_39_S39_R2_001 | 94.8% | 57% | 15.3 |
| pH6_40_S40_R1_001 | 96.3% | 57% | 12.7 |
| pH6_40_S40_R2_001 | 94.5% | 56% | 12.7 |
| pH6_41_S41_R1_001 | 95.1% | 57% | 12.9 |
| pH6_41_S41_R2_001 | 95.3% | 56% | 12.9 |
| pH6_42_S42_R1_001 | 93.6% | 57% | 13.5 |
| pH6_42_S42_R2_001 | 90.6% | 57% | 13.5 |
| pH6_66_S66_R1_001 | 95.6% | 60% | 7.2 |
| pH6_66_S66_R2_001 | 94.4% | 59% | 7.2 |
| pH6_67_S67_R1_001 | 95.4% | 59% | 6.6 |
| pH6_67_S67_R2_001 | 94.1% | 58% | 6.6 |
| pH6_68_S68_R1_001 | 95.2% | 55% | 5.7 |
| pH6_68_S68_R2_001 | 91.0% | 55% | 5.7 |
| pH6_69_S69_R1_001 | 94.8% | 56% | 10.7 |
| pH6_69_S69_R2_001 | 91.5% | 56% | 10.7 |
| pH6ogr_14_S14_R1_001 | 95.7% | 55% | 12.3 |
| pH6ogr_14_S14_R2_001 | 92.3% | 56% | 12.3 |
| pH6ogr_15_S15_R1_001 | 95.2% | 56% | 12.3 |
| pH6ogr_15_S15_R2_001 | 91.7% | 56% | 12.3 |
| pH6ogr_16_S16_R1_001 | 96.3% | 56% | 14.0 |
| pH6ogr_16_S16_R2_001 | 93.5% | 56% | 14.0 |
| pH6ogr_17_S17_R1_001 | 95.8% | 55% | 10.0 |
| pH6ogr_17_S17_R2_001 | 91.8% | 56% | 10.0 |
| pH6ogr_43_S43_R1_001 | 95.5% | 57% | 12.8 |
| pH6ogr_43_S43_R2_001 | 94.7% | 57% | 12.8 |
| pH6ogr_44_S44_R1_001 | 96.2% | 57% | 12.3 |
| pH6ogr_44_S44_R2_001 | 94.1% | 56% | 12.3 |
| pH6ogr_45_S45_R1_001 | 95.7% | 56% | 10.9 |
| pH6ogr_45_S45_R2_001 | 93.3% | 56% | 10.9 |
| pH6ogr_46_S46_R1_001 | 96.8% | 57% | 12.9 |
| pH6ogr_46_S46_R2_001 | 94.3% | 56% | 12.9 |
| pH6ogr_70_S70_R1_001 | 95.5% | 56% | 7.6 |
| pH6ogr_70_S70_R2_001 | 91.4% | 56% | 7.6 |
| pH6ogr_71_S71_R1_001 | 95.6% | 57% | 8.3 |
| pH6ogr_71_S71_R2_001 | 93.4% | 56% | 8.3 |
| pH6ogr_72_S72_R1_001 | 96.4% | 56% | 7.9 |
| pH6ogr_72_S72_R2_001 | 93.5% | 56% | 7.9 |
Variant processing (accepted variants)
This section contains statistics about whether called variants were retained for analysis or not. By default, variants are filtered out if they are not in the designed variants csv.
Variant processing (rejected variants)
This section contains statistics about whether called variants were retained for analysis or not. By default, variants are filtered out if they are not in the designed variants csv.
Variant processing stats
This section contains statistics about whether called variants were retained for analysis or not. By default, variants are filtered out if they are not in the designed variants csv.
GATK
GATK is a toolkit offering a wide variety of tools with a primary focus on variant discovery and genotyping.DOI: 10.1101/201178; 10.1002/0471250953.bi1110s43; 10.1038/ng.806; 10.1101/gr.107524.110.
GATK ASM counts
Per-sample read count and base call fates from GATK AnalyzeSaturationMutagenesis.
This table shows the distribution of calls (for reads or for bases) across all samples. Reads are categorized as WT, a variant, or filtered. Bases can be either evaluated or unevaluated, corresponding to the reads they come from.
Reads are filtered for the following reasons:
- Unmapped: the map quality is below the minimum MapQ (default = 4)'
- Low quality reads: Reads are trimmed for quality > minQ (default 30) before calling variants. If the final size is less than the minimum length (default 15), or if the remaining segment does not cover the ORF, the read is filtered.
Paired reads are also split into overlapping and disjoint sets, with further filters for both.
- Inconsistent: If overlapping reads disagree on the called variant, the read is filtered.
- Ignored mate: If the pairs are disjoint, the first read of the pair is used for analysis, and the second is ignored.
- Low quality variation: If the variant includes ambiguous bases (not A, C, G, or T, or -), the read is filtered.
- Insufficient flank: If the variant does not include a certain number of WT bases (default 2) flanking the variant, the read is filtered.
| Sample Name | Total reads (M) | WT reads (M) | Variant reads (M) | Filtered reads (M) |
|---|---|---|---|---|
| nontreated_R1 | 37.3 | 14.9 | 2.7 | 7.6 |
| nontreated_R2 | 26.5 | 10.5 | 1.8 | 6.2 |
| ph55_R1_B1 | 25.2 | 10.1 | 1.7 | 5.6 |
| ph55_R1_B2 | 29.4 | 12.0 | 2.0 | 5.0 |
| ph55_R1_B3 | 25.3 | 10.2 | 1.7 | 5.9 |
| ph55_R1_B4 | 21.0 | 8.6 | 1.3 | 5.8 |
| ph55_R2_B1 | 27.5 | 11.0 | 1.8 | 6.0 |
| ph55_R2_B2 | 26.0 | 10.4 | 1.8 | 5.4 |
| ph55_R2_B3 | 25.2 | 10.3 | 1.6 | 3.6 |
| ph55_R2_B4 | 25.3 | 10.5 | 1.5 | 4.0 |
| ph55_R3_B1 | 26.3 | 10.7 | 1.8 | 5.8 |
| ph55_R3_B2 | 24.2 | 9.8 | 1.6 | 4.7 |
| ph55_R3_B3 | 27.5 | 11.3 | 1.8 | 4.9 |
| ph55_R3_B4 | 21.3 | 8.8 | 1.2 | 4.6 |
| ph55_ogr_R1_B1 | 37.1 | 14.8 | 2.6 | 8.0 |
| ph55_ogr_R1_B2 | 24.6 | 9.8 | 1.7 | 6.1 |
| ph55_ogr_R1_B3 | 22.1 | 8.7 | 1.5 | 5.9 |
| ph55_ogr_R1_B4 | 16.6 | 6.8 | 1.0 | 2.8 |
| ph55_ogr_R2_B1 | 20.0 | 7.9 | 1.3 | 5.0 |
| ph55_ogr_R2_B2 | 26.9 | 10.8 | 1.9 | 5.4 |
| ph55_ogr_R2_B3 | 29.5 | 12.0 | 2.0 | 5.3 |
| ph55_ogr_R2_B4 | 23.2 | 9.3 | 1.5 | 5.8 |
| ph55_ogr_R3_B1 | 26.8 | 10.9 | 1.8 | 4.4 |
| ph55_ogr_R3_B2 | 32.0 | 12.8 | 2.0 | 7.3 |
| ph55_ogr_R3_B4 | 13.8 | 5.7 | 0.8 | 3.1 |
| ph65_R1_B1 | 19.5 | 7.6 | 1.1 | 6.5 |
| ph65_R1_B2 | 26.8 | 10.7 | 1.8 | 7.0 |
| ph65_R1_B3 | 24.4 | 9.8 | 1.6 | 6.0 |
| ph65_R1_B4 | 13.9 | 5.9 | 0.8 | 0.8 |
| ph65_R2_B1 | 25.2 | 10.2 | 1.7 | 5.3 |
| ph65_R2_B2 | 30.4 | 12.2 | 2.1 | 6.2 |
| ph65_R2_B3 | 31.8 | 12.8 | 2.2 | 7.0 |
| ph65_R2_B4 | 14.9 | 6.2 | 0.9 | 2.0 |
| ph65_R3_B1 | 14.5 | 6.0 | 0.9 | 2.1 |
| ph65_R3_B2 | 12.3 | 5.0 | 0.8 | 2.9 |
| ph65_R3_B3 | 12.5 | 5.2 | 0.8 | 1.5 |
| ph65_R3_B4 | 8.7 | 3.6 | 0.5 | 1.4 |
| ph65_ogr_R1_B1 | 18.7 | 7.4 | 1.3 | 4.8 |
| ph65_ogr_R1_B2 | 24.4 | 9.8 | 1.6 | 4.7 |
| ph65_ogr_R1_B3 | 20.7 | 8.4 | 1.3 | 3.9 |
| ph65_ogr_R1_B4 | 18.0 | 7.5 | 1.0 | 2.4 |
| ph65_ogr_R2_B1 | 28.8 | 11.7 | 2.0 | 5.7 |
| ph65_ogr_R2_B2 | 24.3 | 9.7 | 1.7 | 5.5 |
| ph65_ogr_R2_B3 | 21.3 | 8.6 | 1.3 | 4.9 |
| ph65_ogr_R2_B4 | 24.5 | 10.2 | 1.4 | 5.5 |
| ph65_ogr_R3_B1 | 13.0 | 5.2 | 0.9 | 3.6 |
| ph65_ogr_R3_B2 | 14.0 | 5.6 | 0.9 | 3.6 |
| ph65_ogr_R3_B3 | 16.3 | 6.6 | 1.1 | 3.8 |
| ph65_ogr_R3_B4 | 11.3 | 4.7 | 0.6 | 2.0 |
| ph6_R1_B1 | 24.6 | 9.8 | 1.6 | 6.3 |
| ph6_R1_B2 | 22.5 | 8.9 | 1.6 | 5.3 |
| ph6_R1_B3 | 28.1 | 11.3 | 1.9 | 6.0 |
| ph6_R1_B4 | 20.0 | 8.4 | 1.1 | 1.7 |
| ph6_R2_B1 | 28.8 | 11.7 | 1.9 | 4.8 |
| ph6_R2_B2 | 24.1 | 9.7 | 1.7 | 4.8 |
| ph6_R2_B3 | 24.4 | 9.8 | 1.4 | 5.2 |
| ph6_R2_B4 | 17.9 | 7.5 | 1.1 | 3.8 |
| ph6_R3_B1 | 13.1 | 5.4 | 0.8 | 1.4 |
| ph6_R3_B2 | 12.0 | 5.0 | 0.8 | 1.6 |
| ph6_R3_B3 | 11.1 | 4.5 | 0.7 | 3.4 |
| ph6_R3_B4 | 19.0 | 7.6 | 1.3 | 4.6 |
| ph6_ogr_R1_B1 | 23.5 | 9.4 | 1.6 | 6.3 |
| ph6_ogr_R1_B2 | 23.4 | 9.2 | 1.5 | 5.9 |
| ph6_ogr_R1_B3 | 26.7 | 10.8 | 1.9 | 5.8 |
| ph6_ogr_R1_B4 | 18.8 | 7.7 | 1.1 | 5.1 |
| ph6_ogr_R2_B1 | 24.3 | 9.8 | 1.6 | 4.8 |
| ph6_ogr_R2_B2 | 23.4 | 9.4 | 1.7 | 4.6 |
| ph6_ogr_R2_B3 | 20.9 | 8.3 | 1.4 | 5.2 |
| ph6_ogr_R2_B4 | 24.4 | 10.1 | 1.5 | 5.1 |
| ph6_ogr_R3_B1 | 14.6 | 5.8 | 1.0 | 3.7 |
| ph6_ogr_R3_B3 | 15.7 | 6.4 | 1.0 | 3.4 |
| ph6_ogr_R3_B4 | 15.2 | 6.3 | 0.9 | 3.5 |
| surface_R1_B1 | 20.3 | 8.0 | 1.4 | 5.7 |
| surface_R1_B2 | 25.3 | 10.0 | 1.8 | 6.8 |
| surface_R1_B3 | 26.8 | 10.9 | 1.7 | 6.4 |
| surface_R1_B4 | 17.7 | 7.2 | 1.0 | 5.2 |
| surface_R2_B1 | 27.7 | 11.1 | 1.9 | 5.7 |
| surface_R2_B2 | 22.8 | 9.1 | 1.6 | 4.3 |
| surface_R2_B3 | 17.8 | 7.2 | 1.2 | 4.7 |
| surface_R2_B4 | 22.8 | 9.2 | 1.4 | 6.4 |
| surface_R3_B1 | 14.2 | 5.6 | 0.9 | 3.6 |
| surface_R3_B2 | 16.4 | 6.7 | 1.1 | 2.5 |
| surface_R3_B4 | 16.5 | 6.8 | 1.0 | 2.1 |
Read counts
Read counts and read fate. Filtered reads include unmapped, low quality, and other pathologies.
Reads can be filtered by GATK AnalyzeSaturationMutagenesis for a number of reasons, including low quality, insufficient flank, and other pathologies. This plot shows the number of reads that were mapped to WT, called as variants, and the number that were filtered.
Base calls
Base calls evaluated for variants and base calls not evaluated for variants.
Bases can be filtered by GATK AnalyzeSaturationMutagenesis for a number of reasons, including low quality, insufficient flank, and other pathologies. This plot shows the number of base calls that were evaluated for variants and the number of base calls that were not evaluated for variants.
BBTools
BBTools is a suite of fast multithreaded bioinformatics tools designed for the analysis of DNA and RNA sequence data.
BBDuk filtering statistics summary table
Proportion of reads that matched adapters/contaminants.
| Sample Name | Percent filtered |
|---|---|
| nontreated_R1 | 0.0% |
| nontreated_R2 | 23.0% |
| ph55_R1_B1 | 25.0% |
| ph55_R1_B2 | 0.0% |
| ph55_R1_B3 | 22.9% |
| ph55_R1_B4 | 16.8% |
| ph55_R2_B1 | 24.8% |
| ph55_R2_B2 | 0.0% |
| ph55_R2_B3 | 37.9% |
| ph55_R2_B4 | 33.4% |
| ph55_R3_B1 | 0.0% |
| ph55_R3_B2 | 0.0% |
| ph55_R3_B3 | 0.0% |
| ph55_R3_B4 | 0.0% |
| ph55_ogr_R1_B1 | 0.0% |
| ph55_ogr_R1_B2 | 21.4% |
| ph55_ogr_R1_B3 | 19.1% |
| ph55_ogr_R1_B4 | 31.6% |
| ph55_ogr_R2_B1 | 21.6% |
| ph55_ogr_R2_B2 | 0.0% |
| ph55_ogr_R2_B3 | 31.4% |
| ph55_ogr_R2_B4 | 20.5% |
| ph55_ogr_R3_B1 | 32.7% |
| ph55_ogr_R3_B2 | 0.0% |
| ph55_ogr_R3_B4 | 24.7% |
| ph65_R1_B1 | 14.0% |
| ph65_R1_B2 | 18.9% |
| ph65_R1_B3 | 21.8% |
| ph65_R1_B4 | 64.9% |
| ph65_R2_B1 | 26.5% |
| ph65_R2_B2 | 27.0% |
| ph65_R2_B3 | 24.6% |
| ph65_R2_B4 | 43.8% |
| ph65_R3_B1 | 39.3% |
| ph65_R3_B2 | 0.0% |
| ph65_R3_B3 | 0.0% |
| ph65_R3_B4 | 37.6% |
| ph65_ogr_R1_B1 | 19.5% |
| ph65_ogr_R1_B2 | 0.0% |
| ph65_ogr_R1_B3 | 29.2% |
| ph65_ogr_R1_B4 | 0.0% |
| ph65_ogr_R2_B1 | 28.3% |
| ph65_ogr_R2_B2 | 0.0% |
| ph65_ogr_R2_B3 | 24.0% |
| ph65_ogr_R2_B4 | 23.4% |
| ph65_ogr_R3_B1 | 16.8% |
| ph65_ogr_R3_B2 | 0.0% |
| ph65_ogr_R3_B3 | 22.4% |
| ph65_ogr_R3_B4 | 29.9% |
| ph6_R1_B1 | 21.1% |
| ph6_R1_B2 | 0.0% |
| ph6_R1_B3 | 25.8% |
| ph6_R1_B4 | 53.6% |
| ph6_R2_B1 | 33.4% |
| ph6_R2_B2 | 26.3% |
| ph6_R2_B3 | 27.6% |
| ph6_R2_B4 | 27.8% |
| ph6_R3_B1 | 44.8% |
| ph6_R3_B2 | 39.4% |
| ph6_R3_B3 | 14.3% |
| ph6_R3_B4 | 20.5% |
| ph6_ogr_R1_B1 | 18.9% |
| ph6_ogr_R1_B2 | 22.4% |
| ph6_ogr_R1_B3 | 24.1% |
| ph6_ogr_R1_B4 | 17.6% |
| ph6_ogr_R2_B1 | 0.0% |
| ph6_ogr_R2_B2 | 25.9% |
| ph6_ogr_R2_B3 | 0.0% |
| ph6_ogr_R2_B4 | 0.0% |
| ph6_ogr_R3_B1 | 20.3% |
| ph6_ogr_R3_B3 | 25.6% |
| ph6_ogr_R3_B4 | 22.4% |
| surface_R1_B1 | 16.3% |
| surface_R1_B2 | 17.3% |
| surface_R1_B3 | 0.0% |
| surface_R1_B4 | 0.0% |
| surface_R2_B1 | 26.9% |
| surface_R2_B2 | 0.0% |
| surface_R2_B3 | 18.9% |
| surface_R2_B4 | 17.2% |
| surface_R3_B1 | 20.0% |
| surface_R3_B2 | 34.5% |
| surface_R3_B4 | 41.7% |
Identity histogram
Histogram of read count versus percent base pair identity of aligned reads (idhist).
Identity histogram summary table
Histogram of read count versus percent base pair identity of aligned reads (idhist).
| Sample Name | Mean_reads | Mean_bases | Median_reads | Median_bases | Mode_reads | Mode_bases | STDev_reads | STDev_bases |
|---|---|---|---|---|---|---|---|---|
| nontreated_R1 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.5 |
| nontreated_R2 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.4 | 7.5 |
| ph55_R1_B1 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| ph55_R1_B2 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.9 |
| ph55_R1_B3 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.3 | 7.4 |
| ph55_R1_B4 | 97.8 | 97.8 | 100.0 | 100.0 | 100.0 | 100.0 | 6.7 | 6.8 |
| ph55_R2_B1 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph55_R2_B2 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.9 |
| ph55_R2_B3 | 97.4 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| ph55_R2_B4 | 97.8 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.8 | 7.0 |
| ph55_R3_B1 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| ph55_R3_B2 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| ph55_R3_B3 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph55_R3_B4 | 97.7 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.9 | 7.0 |
| ph55_ogr_R1_B1 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.8 |
| ph55_ogr_R1_B2 | 97.2 | 97.1 | 100.0 | 100.0 | 100.0 | 100.0 | 7.9 | 7.9 |
| ph55_ogr_R1_B3 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.4 | 7.5 |
| ph55_ogr_R1_B4 | 97.7 | 97.6 | 100.0 | 100.0 | 100.0 | 100.0 | 7.0 | 7.1 |
| ph55_ogr_R2_B1 | 97.2 | 97.1 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.9 |
| ph55_ogr_R2_B2 | 97.2 | 97.1 | 100.0 | 100.0 | 100.0 | 100.0 | 7.9 | 8.0 |
| ph55_ogr_R2_B3 | 97.4 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| ph55_ogr_R2_B4 | 97.7 | 97.6 | 100.0 | 100.0 | 100.0 | 100.0 | 6.8 | 6.9 |
| ph55_ogr_R3_B1 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.9 |
| ph55_ogr_R3_B2 | 97.2 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.9 |
| ph55_ogr_R3_B4 | 97.8 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.8 | 6.9 |
| ph65_R1_B1 | 97.3 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.3 | 7.3 |
| ph65_R1_B2 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.5 |
| ph65_R1_B3 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph65_R1_B4 | 97.5 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 8.0 |
| ph65_R2_B1 | 97.4 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.4 | 7.5 |
| ph65_R2_B2 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.4 | 7.5 |
| ph65_R2_B3 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph65_R2_B4 | 97.5 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph65_R3_B1 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.4 | 7.6 |
| ph65_R3_B2 | 97.4 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.5 |
| ph65_R3_B3 | 97.5 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph65_R3_B4 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.9 |
| ph65_ogr_R1_B1 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| ph65_ogr_R1_B2 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| ph65_ogr_R1_B3 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.3 | 7.4 |
| ph65_ogr_R1_B4 | 97.8 | 97.6 | 100.0 | 100.0 | 100.0 | 100.0 | 6.9 | 7.1 |
| ph65_ogr_R2_B1 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| ph65_ogr_R2_B2 | 97.3 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph65_ogr_R2_B3 | 97.4 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| ph65_ogr_R2_B4 | 97.8 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.9 | 7.0 |
| ph65_ogr_R3_B1 | 97.3 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| ph65_ogr_R3_B2 | 97.2 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph65_ogr_R3_B3 | 97.3 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph65_ogr_R3_B4 | 97.7 | 97.6 | 100.0 | 100.0 | 100.0 | 100.0 | 7.1 | 7.2 |
| ph6_R1_B1 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.4 | 7.4 |
| ph6_R1_B2 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.5 |
| ph6_R1_B3 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.3 | 7.4 |
| ph6_R1_B4 | 97.7 | 97.5 | 100.0 | 100.0 | 100.0 | 100.0 | 7.2 | 7.4 |
| ph6_R2_B1 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| ph6_R2_B2 | 97.4 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.6 |
| ph6_R2_B3 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph6_R2_B4 | 97.8 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.9 | 7.0 |
| ph6_R3_B1 | 97.4 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.8 |
| ph6_R3_B2 | 97.5 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph6_R3_B3 | 97.3 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.6 |
| ph6_R3_B4 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.3 | 7.4 |
| ph6_ogr_R1_B1 | 97.3 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.6 |
| ph6_ogr_R1_B2 | 97.2 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph6_ogr_R1_B3 | 97.5 | 97.4 | 100.0 | 100.0 | 100.0 | 100.0 | 7.3 | 7.4 |
| ph6_ogr_R1_B4 | 97.7 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.9 | 6.9 |
| ph6_ogr_R2_B1 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph6_ogr_R2_B2 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| ph6_ogr_R2_B3 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| ph6_ogr_R2_B4 | 97.8 | 97.8 | 100.0 | 100.0 | 100.0 | 100.0 | 6.7 | 6.8 |
| ph6_ogr_R3_B1 | 97.2 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| ph6_ogr_R3_B3 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| ph6_ogr_R3_B4 | 97.7 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.9 | 7.0 |
| surface_R1_B1 | 97.2 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.8 |
| surface_R1_B2 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.6 | 7.7 |
| surface_R1_B3 | 97.7 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.9 | 7.0 |
| surface_R1_B4 | 97.8 | 97.8 | 100.0 | 100.0 | 100.0 | 100.0 | 6.6 | 6.7 |
| surface_R2_B1 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.8 | 7.9 |
| surface_R2_B2 | 97.4 | 97.3 | 100.0 | 100.0 | 100.0 | 100.0 | 7.5 | 7.6 |
| surface_R2_B3 | 97.6 | 97.6 | 100.0 | 100.0 | 100.0 | 100.0 | 7.0 | 7.0 |
| surface_R2_B4 | 97.7 | 97.7 | 100.0 | 100.0 | 100.0 | 100.0 | 6.7 | 6.8 |
| surface_R3_B1 | 97.2 | 97.1 | 100.0 | 100.0 | 100.0 | 100.0 | 7.9 | 7.9 |
| surface_R3_B2 | 97.3 | 97.2 | 100.0 | 100.0 | 100.0 | 100.0 | 7.7 | 7.8 |
| surface_R3_B4 | 97.7 | 97.5 | 100.0 | 100.0 | 100.0 | 100.0 | 7.0 | 7.2 |
Indel lengths
Indel length histogram (indelhist). The plots show the number of observed insertions and deletions, for each insertion and deletion length.
Match, substitution, deletion, and insertion rates
Histogram of match, substitution, deleletion, and insertion rates by read location (mhist).
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Read quality
Histogram of average read qualities (aqhist). Plot shows the number of reads at each quality score.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Errors-per-read
Errors-per-read histogram (ehist).
Read lengths
Read length histogram (lhist).
Insert sizes
Histogram of computed insert sizes, for paired reads (ihist). Plotted data has been cut off at 99% to prevent long tails; Complete data available in original source files.
The insert size is the length of the sequence between the sequencing adapters, which for most common insert sizes is longer than the sum of both read pairs. In some cases, the insert size is shorter than the length of the two read pairs combined, resulting in an insert size shorter than the sum of the length of the reads pairs.
Insert sizes summary table
Histogram of computed insert sizes, for paired reads (ihist). Plotted data has been cut off at 99% to prevent long tails; Complete data available in original source files.
The insert size is the length of the sequence between the sequencing adapters, which for most common insert sizes is longer than the sum of both read pairs. In some cases, the insert size is shorter than the length of the two read pairs combined, resulting in an insert size shorter than the sum of the length of the reads pairs.
| Sample Name | Mean | Median | STDev | PercentOfPairs |
|---|---|---|---|---|
| nontreated_R1 | 160.0 | 158.0 | 68.7 | 61.0 |
| nontreated_R2 | 163.4 | 163.0 | 70.4 | 55.6 |
| ph55_R1_B1 | 160.2 | 158.0 | 70.4 | 57.4 |
| ph55_R1_B2 | 153.4 | 148.0 | 69.1 | 67.9 |
| ph55_R1_B3 | 162.2 | 161.0 | 69.5 | 54.6 |
| ph55_R1_B4 | 169.9 | 171.0 | 68.7 | 45.1 |
| ph55_R2_B1 | 162.1 | 161.0 | 69.5 | 59.2 |
| ph55_R2_B2 | 160.5 | 159.0 | 69.6 | 60.2 |
| ph55_R2_B3 | 148.4 | 141.0 | 69.1 | 75.0 |
| ph55_R2_B4 | 153.5 | 149.0 | 69.5 | 70.7 |
| ph55_R3_B1 | 160.4 | 158.0 | 70.5 | 57.3 |
| ph55_R3_B2 | 157.7 | 155.0 | 70.1 | 63.4 |
| ph55_R3_B3 | 153.5 | 149.0 | 70.6 | 65.6 |
| ph55_R3_B4 | 162.2 | 161.0 | 70.6 | 59.9 |
| ph55_ogr_R1_B1 | 159.4 | 157.0 | 69.1 | 59.2 |
| ph55_ogr_R1_B2 | 163.5 | 162.0 | 69.5 | 51.8 |
| ph55_ogr_R1_B3 | 167.1 | 168.0 | 69.5 | 49.1 |
| ph55_ogr_R1_B4 | 156.6 | 153.0 | 68.5 | 70.2 |
| ph55_ogr_R2_B1 | 164.5 | 164.0 | 70.0 | 53.3 |
| ph55_ogr_R2_B2 | 158.7 | 156.0 | 69.8 | 61.7 |
| ph55_ogr_R2_B3 | 153.2 | 148.0 | 69.5 | 65.8 |
| ph55_ogr_R2_B4 | 165.3 | 166.0 | 70.8 | 50.8 |
| ph55_ogr_R3_B1 | 153.9 | 149.0 | 69.6 | 69.5 |
| ph55_ogr_R3_B2 | 164.7 | 164.0 | 70.3 | 57.0 |
| ph55_ogr_R3_B4 | 161.1 | 160.0 | 70.5 | 58.0 |
| ph65_R1_B1 | 171.6 | 174.0 | 70.1 | 38.2 |
| ph65_R1_B2 | 167.8 | 168.0 | 69.3 | 49.0 |
| ph65_R1_B3 | 163.9 | 163.0 | 70.0 | 53.1 |
| ph65_R1_B4 | 117.0 | 103.0 | 62.1 | 90.9 |
| ph65_R2_B1 | 158.3 | 156.0 | 70.2 | 59.7 |
| ph65_R2_B2 | 158.2 | 155.0 | 70.5 | 60.5 |
| ph65_R2_B3 | 161.3 | 160.0 | 69.7 | 58.0 |
| ph65_R2_B4 | 140.3 | 130.0 | 69.9 | 77.8 |
| ph65_R3_B1 | 144.3 | 136.0 | 69.5 | 73.5 |
| ph65_R3_B2 | 166.5 | 167.0 | 69.4 | 54.4 |
| ph65_R3_B3 | 145.2 | 137.0 | 69.0 | 78.5 |
| ph65_R3_B4 | 146.6 | 139.0 | 69.8 | 72.3 |
| ph65_ogr_R1_B1 | 166.7 | 167.0 | 69.4 | 49.7 |
| ph65_ogr_R1_B2 | 155.7 | 152.0 | 69.5 | 63.7 |
| ph65_ogr_R1_B3 | 158.1 | 155.0 | 68.8 | 66.0 |
| ph65_ogr_R1_B4 | 142.8 | 134.0 | 68.4 | 77.7 |
| ph65_ogr_R2_B1 | 156.2 | 152.0 | 70.2 | 61.8 |
| ph65_ogr_R2_B2 | 167.3 | 168.0 | 69.4 | 56.5 |
| ph65_ogr_R2_B3 | 163.2 | 162.0 | 70.9 | 57.7 |
| ph65_ogr_R2_B4 | 163.1 | 162.0 | 70.9 | 56.1 |
| ph65_ogr_R3_B1 | 171.8 | 174.0 | 69.5 | 46.1 |
| ph65_ogr_R3_B2 | 166.0 | 166.0 | 70.0 | 50.5 |
| ph65_ogr_R3_B3 | 163.4 | 162.0 | 69.9 | 54.2 |
| ph65_ogr_R3_B4 | 157.8 | 155.0 | 69.3 | 67.0 |
| ph6_R1_B1 | 164.1 | 164.0 | 69.7 | 51.8 |
| ph6_R1_B2 | 163.8 | 163.0 | 69.2 | 55.9 |
| ph6_R1_B3 | 159.2 | 157.0 | 69.5 | 58.8 |
| ph6_R1_B4 | 131.3 | 120.0 | 65.2 | 86.7 |
| ph6_R2_B1 | 152.1 | 147.0 | 69.2 | 69.2 |
| ph6_R2_B2 | 161.0 | 159.0 | 69.2 | 61.4 |
| ph6_R2_B3 | 157.6 | 155.0 | 69.8 | 61.6 |
| ph6_R2_B4 | 155.7 | 151.0 | 70.6 | 60.0 |
| ph6_R3_B1 | 141.4 | 132.0 | 68.4 | 81.5 |
| ph6_R3_B2 | 146.2 | 138.0 | 69.8 | 75.7 |
| ph6_R3_B3 | 170.9 | 173.0 | 70.4 | 38.4 |
| ph6_R3_B4 | 167.2 | 168.0 | 70.2 | 52.4 |
| ph6_ogr_R1_B1 | 166.4 | 167.0 | 69.9 | 47.7 |
| ph6_ogr_R1_B2 | 162.4 | 161.0 | 69.3 | 53.5 |
| ph6_ogr_R1_B3 | 162.7 | 162.0 | 70.0 | 57.6 |
| ph6_ogr_R1_B4 | 167.8 | 169.0 | 69.8 | 45.5 |
| ph6_ogr_R2_B1 | 156.1 | 152.0 | 69.6 | 63.7 |
| ph6_ogr_R2_B2 | 161.6 | 160.0 | 69.6 | 61.4 |
| ph6_ogr_R2_B3 | 162.3 | 161.0 | 70.4 | 52.8 |
| ph6_ogr_R2_B4 | 158.1 | 155.0 | 69.8 | 59.5 |
| ph6_ogr_R3_B1 | 165.4 | 165.0 | 70.4 | 50.2 |
| ph6_ogr_R3_B3 | 159.5 | 157.0 | 69.8 | 58.5 |
| ph6_ogr_R3_B4 | 163.0 | 162.0 | 69.6 | 54.2 |
| surface_R1_B1 | 173.8 | 177.0 | 69.9 | 46.2 |
| surface_R1_B2 | 171.0 | 173.0 | 68.7 | 47.2 |
| surface_R1_B3 | 167.3 | 168.0 | 69.6 | 53.3 |
| surface_R1_B4 | 171.2 | 173.0 | 70.0 | 43.0 |
| surface_R2_B1 | 158.4 | 156.0 | 69.8 | 60.8 |
| surface_R2_B2 | 159.5 | 157.0 | 69.2 | 64.3 |
| surface_R2_B3 | 166.4 | 167.0 | 70.5 | 47.7 |
| surface_R2_B4 | 169.6 | 171.0 | 69.9 | 45.6 |
| surface_R3_B1 | 167.1 | 168.0 | 70.4 | 51.3 |
| surface_R3_B2 | 152.1 | 147.0 | 69.8 | 71.3 |
| surface_R3_B4 | 143.6 | 135.0 | 70.0 | 77.4 |
GC content
Read GC content histogram (gchist).
GC content summary table
Read GC content histogram (gchist).
| Sample Name | Mean | Median | Mode | STDev |
|---|---|---|---|---|
| nontreated_R1 | 56.8 | 53.6 | 52.4 | 7.1 |
| nontreated_R2 | 56.3 | 53.4 | 52.4 | 6.8 |
| ph55_R1_B1 | 57.0 | 53.6 | 52.4 | 7.3 |
| ph55_R1_B2 | 57.7 | 54.2 | 52.4 | 7.6 |
| ph55_R1_B3 | 56.3 | 53.4 | 52.4 | 6.8 |
| ph55_R1_B4 | 55.4 | 53.0 | 52.4 | 6.1 |
| ph55_R2_B1 | 56.9 | 53.6 | 52.4 | 7.2 |
| ph55_R2_B2 | 57.0 | 53.6 | 52.4 | 7.2 |
| ph55_R2_B3 | 59.0 | 55.6 | 52.4 | 8.2 |
| ph55_R2_B4 | 58.4 | 54.8 | 52.4 | 8.1 |
| ph55_R3_B1 | 56.9 | 53.6 | 52.4 | 7.2 |
| ph55_R3_B2 | 57.7 | 54.2 | 52.4 | 7.7 |
| ph55_R3_B3 | 57.5 | 54.0 | 52.4 | 7.5 |
| ph55_R3_B4 | 56.7 | 53.6 | 52.4 | 7.1 |
| ph55_ogr_R1_B1 | 56.8 | 53.6 | 52.4 | 7.1 |
| ph55_ogr_R1_B2 | 56.5 | 53.4 | 52.4 | 7.0 |
| ph55_ogr_R1_B3 | 56.0 | 53.2 | 52.4 | 6.5 |
| ph55_ogr_R1_B4 | 57.6 | 54.2 | 52.4 | 7.5 |
| ph55_ogr_R2_B1 | 56.2 | 53.4 | 52.4 | 6.8 |
| ph55_ogr_R2_B2 | 57.2 | 53.8 | 52.4 | 7.4 |
| ph55_ogr_R2_B3 | 58.1 | 54.4 | 52.4 | 7.9 |
| ph55_ogr_R2_B4 | 56.2 | 53.2 | 52.4 | 6.8 |
| ph55_ogr_R3_B1 | 58.3 | 54.6 | 52.4 | 8.0 |
| ph55_ogr_R3_B2 | 56.7 | 53.6 | 52.4 | 7.2 |
| ph55_ogr_R3_B4 | 56.6 | 53.4 | 52.4 | 7.1 |
| ph65_R1_B1 | 55.4 | 53.2 | 52.4 | 6.1 |
| ph65_R1_B2 | 55.9 | 53.2 | 52.4 | 6.5 |
| ph65_R1_B3 | 56.6 | 53.4 | 52.4 | 7.0 |
| ph65_R1_B4 | 64.8 | 65.4 | 52.4 | 9.3 |
| ph65_R2_B1 | 57.2 | 53.8 | 52.4 | 7.5 |
| ph65_R2_B2 | 57.3 | 53.8 | 52.4 | 7.5 |
| ph65_R2_B3 | 57.0 | 53.6 | 52.4 | 7.3 |
| ph65_R2_B4 | 61.0 | 59.6 | 52.4 | 9.4 |
| ph65_R3_B1 | 59.2 | 56.2 | 52.4 | 8.4 |
| ph65_R3_B2 | 56.6 | 53.6 | 52.4 | 6.9 |
| ph65_R3_B3 | 59.8 | 57.0 | 52.4 | 8.5 |
| ph65_R3_B4 | 59.4 | 57.2 | 52.4 | 9.1 |
| ph65_ogr_R1_B1 | 55.7 | 53.2 | 52.4 | 6.3 |
| ph65_ogr_R1_B2 | 57.7 | 54.2 | 52.4 | 7.7 |
| ph65_ogr_R1_B3 | 57.7 | 54.2 | 52.4 | 7.6 |
| ph65_ogr_R1_B4 | 59.7 | 57.8 | 52.4 | 8.7 |
| ph65_ogr_R2_B1 | 57.2 | 53.8 | 52.4 | 7.4 |
| ph65_ogr_R2_B2 | 56.2 | 53.4 | 52.4 | 6.7 |
| ph65_ogr_R2_B3 | 56.8 | 53.6 | 52.4 | 7.2 |
| ph65_ogr_R2_B4 | 56.9 | 53.8 | 52.4 | 7.5 |
| ph65_ogr_R3_B1 | 55.7 | 53.2 | 52.4 | 6.3 |
| ph65_ogr_R3_B2 | 56.2 | 53.4 | 52.4 | 6.7 |
| ph65_ogr_R3_B3 | 56.4 | 53.4 | 52.4 | 6.8 |
| ph65_ogr_R3_B4 | 57.6 | 54.6 | 52.4 | 7.6 |
| ph6_R1_B1 | 56.6 | 53.6 | 52.4 | 7.0 |
| ph6_R1_B2 | 56.7 | 53.6 | 52.4 | 7.1 |
| ph6_R1_B3 | 56.8 | 53.6 | 52.4 | 7.1 |
| ph6_R1_B4 | 62.4 | 61.6 | 52.4 | 9.2 |
| ph6_R2_B1 | 58.1 | 54.4 | 52.4 | 7.8 |
| ph6_R2_B2 | 56.9 | 53.6 | 52.4 | 7.1 |
| ph6_R2_B3 | 57.1 | 53.8 | 52.4 | 7.4 |
| ph6_R2_B4 | 57.5 | 54.6 | 52.4 | 8.1 |
| ph6_R3_B1 | 60.1 | 57.6 | 52.0 | 8.5 |
| ph6_R3_B2 | 59.0 | 55.8 | 52.4 | 8.2 |
| ph6_R3_B3 | 55.1 | 53.0 | 52.4 | 5.8 |
| ph6_R3_B4 | 56.2 | 53.4 | 52.4 | 6.8 |
| ph6_ogr_R1_B1 | 55.9 | 53.2 | 52.4 | 6.5 |
| ph6_ogr_R1_B2 | 56.2 | 53.4 | 52.4 | 6.7 |
| ph6_ogr_R1_B3 | 56.5 | 53.4 | 52.4 | 7.0 |
| ph6_ogr_R1_B4 | 56.2 | 53.4 | 52.4 | 6.9 |
| ph6_ogr_R2_B1 | 57.7 | 54.0 | 52.4 | 7.7 |
| ph6_ogr_R2_B2 | 57.0 | 53.6 | 52.4 | 7.3 |
| ph6_ogr_R2_B3 | 56.7 | 53.6 | 52.4 | 7.1 |
| ph6_ogr_R2_B4 | 56.9 | 53.6 | 52.4 | 7.2 |
| ph6_ogr_R3_B1 | 56.4 | 53.4 | 52.4 | 6.8 |
| ph6_ogr_R3_B3 | 57.3 | 53.8 | 52.4 | 7.4 |
| ph6_ogr_R3_B4 | 56.5 | 53.4 | 52.4 | 6.9 |
| surface_R1_B1 | 55.3 | 53.0 | 52.4 | 5.9 |
| surface_R1_B2 | 56.0 | 53.4 | 52.4 | 6.5 |
| surface_R1_B3 | 55.9 | 53.2 | 52.4 | 6.4 |
| surface_R1_B4 | 55.3 | 53.0 | 52.4 | 6.0 |
| surface_R2_B1 | 57.2 | 53.8 | 52.4 | 7.5 |
| surface_R2_B2 | 57.7 | 54.2 | 52.4 | 7.8 |
| surface_R2_B3 | 56.0 | 53.2 | 52.4 | 6.6 |
| surface_R2_B4 | 55.8 | 53.2 | 52.4 | 6.4 |
| surface_R3_B1 | 55.9 | 53.2 | 52.4 | 6.5 |
| surface_R3_B2 | 58.6 | 55.0 | 52.4 | 8.0 |
| surface_R3_B4 | 60.0 | 56.8 | 52.4 | 8.6 |
Base composition
Base composition histogram by position (bhist). The plot shows the percentage of G+C, A+T, and N bases for each position in the reads.
Relative composition
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
FastQC
0.12.1
FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.
Sequence Counts
Sequence counts for each sample. Duplicate read counts are an estimate only.
This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).
You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:
Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.
The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Sequence Quality Histograms
The mean quality value across each base position in the read.
To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).
Taken from the FastQC help:
The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Per Sequence Quality Scores
The number of reads with average quality scores. Shows if a subset of reads has poor quality.
From the FastQC help:
The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Per Base Sequence Content
The proportion of each base position for which each of the four normal DNA bases has been called.
To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.
To see the data as a line plot, as in the original FastQC graph, click on a sample track.
From the FastQC help:
Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.
In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.
It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.
Rollover for sample name
Per Sequence GC Content
The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.
From the FastQC help:
This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.
In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.
An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Per Base N Content
The percentage of base calls at each position for which an N was called.
From the FastQC help:
If a sequencer is unable to make a base call with sufficient confidence then it will
normally substitute an N rather than a conventional base call. This graph shows the
percentage of base calls at each position for which an N was called.
It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Sequence Length Distribution
Sequence Duplication Levels
The relative level of duplication found for every sequence.
From the FastQC Help:
In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.
Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.
The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.
In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Overrepresented sequences by sample
The total amount of overrepresented sequences found in each library.
FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.
Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.
From the FastQC Help:
A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.
FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Top overrepresented sequences
Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.
| Overrepresented sequence | Samples | Occurrences | % of all reads |
|---|---|---|---|
| GTTCTACATCTGCTCCCTTCCCTTTTGGCTGCAGTACGTCCTCCAGCATG | 166 | 17939525 | 0.9045% |
| GTCTTATACTTGGGTTTGTCTGGTCAACCACCGCGGTCTCCGTCGTCAGG | 166 | 13875976 | 0.6996% |
| GCCCTGGGGACGTCGTCGCGGGTGGCTAAGCGCACCGTGGGCTTGTACTC | 166 | 12305410 | 0.6204% |
| ATGTAGAACAGGTCTGCCACTGTCAGGTTGCACAAGTACACTCCCAACTC | 166 | 12261649 | 0.6182% |
| ACCCTATTCAAGCCTGGCAGCGAGCTATCAATTACTACAGATTTCTCGTG | 166 | 10780616 | 0.5435% |
| CTTCTGACCAGCAGCAACACATGATATGGCAGGAAGCACGCGAGGAAAAT | 166 | 10695012 | 0.5392% |
| GAATAGGGTAGTGCTCGAAGCAGACCCTGTGCTGATTCTCGTCCTCGATC | 166 | 10013724 | 0.5049% |
| GAGCTACATCTTCTGCCTGGTATTCGCCGACTACAAGGACGATGATGACG | 166 | 9148780 | 0.4613% |
| GGTCAGAAGCGTGTGGGAGGCATCTTGTGACTTCGCCAAGGGAGTCTTTA | 166 | 8156703 | 0.4112% |
| GTGCTGAGCACAAGTCTCTGAATTTGGTCTTTGCGAGATTTCTGAGTACC | 166 | 8144354 | 0.4106% |
| ATCCACCAGACCCTCGCTCCCGTGGTTTACGTTACGGTACTTGTCGTAGG | 166 | 7476585 | 0.3770% |
| AAGCAGACCCTGTGCTGATTCTCGTCCTCGATCACTTCCTCGTGCATCAA | 166 | 7291043 | 0.3676% |
| GTATATATTCTCATAAAGAAGAATCCCGCACACTTGGCAGCTCAGGTCAC | 166 | 7566169 | 0.3815% |
| AGCGTGGACCGCTACCTGGCCGTAGCCCATCCTTTCCGATTCCACCAGTT | 166 | 7262512 | 0.3662% |
| GTCCTGGATTTTCCTCCACATCACCAGCTTGTTTCAGTAGACTAAAATTA | 166 | 6923353 | 0.3491% |
| CTACAAGGACGATGATGACGCCAGCATCGATATGGGGAACATCACTGCCG | 166 | 6670813 | 0.3363% |
| CCTCTGGGGCACCCAGCGGATATGCTTCGCGTGCCCTGCCGGTCCTTGAA | 166 | 7196386 | 0.3628% |
| CCATGAAGACGATCATCGCCCTGAGCTACATCTTCTGCCTGGTATTCGCC | 166 | 6755794 | 0.3406% |
| GATTATACCGCAACTACACGCCACCCCGTCAGATCCGGCCACCATGAAGA | 166 | 6619857 | 0.3338% |
| GCGTTAAAGACTCCCTTGGCGAAGTCACAAGATGCCTCCCACACGCTTCT | 166 | 6476300 | 0.3265% |
Adapter Content
The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.
Note that only samples with ≥ 0.1% adapter contamination are shown.
There may be several lines per sample, as one is shown for each adapter detected in the file.
From the FastQC Help:
The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.
Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).
Status Checks
Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).
FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).
It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.
Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.
In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| FastQC | 0.12.1 |